Applying transforms automatically before I export an FBX?
They should be separate objects. Right now, by your explanation, blender sees it as one mesh. 


  different mesh separate inside the same object


They are not different mesh. Blender sees it as one mesh when grouped as object.

In edit mode, select one plane at a time and hit P. Choose selection option. Now it's a separate object you can apply loc,rot,scale to.